Time-Dependent Growth of Gold Nanoparticles: Experimental

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Time Dependent Growth of Gold Nanoparticles: Experimental Corre-lation of van der Waals Contact between DNA and Amino Acids with Polar Uncharged Side Chains Shahbaz Ahmad Lone, and Kalyan K. Sadhu J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.9b04911 • Publication Date (Web): 30 Jul 2019 Downloaded from pubs.acs.org on August 6, 2019

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The Journal of Physical Chemistry

Time Dependent Growth of Gold Nanoparticles: Experimental Correlation of van der Waals Contact between DNA and Amino Acids with Polar Uncharged Side Chains Shahbaz Ahmad Lone,† Kalyan K. Sadhu,*,† †

Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee-247667, Uttarakhand, India

ABSTRACT: Time dependent investigation of growth reactions from 0.45 nM gold nanoparticle seeds in presence of 9 mM amino acids containing polar uncharged side chain (AApusc) serine (Ser), threonine (Thr), asparagine (Asn) and glutamine (Gln) resulted in the formation of aggregated nanostructures either via slow or fast processes. Ser showed immediate aggregation of gold nanoparticles after the growth reaction, while aggregation with Gln, Asn and Thr were much slow. This slow or fast time dependent process was directly related to the van der Waals volumes of these amino acids. The aggregation reaction was inhibited by addition of 600 nM amine modified DNAs (NH2-PR: NH2 (CH2)6-5’-ACATCAGT-3’ and NH2MR: NH2(CH2)6-5’-TCTTCTGT-3’) prior to the addition of 9 mM amino acids before the growth reaction. The van der Waals contact between DNA and amino acids were examined for the controlled growth process after 12 h in presence of the critical concentrations of both DNAs for all the four amino acids. The trend in NH2-PR amount for inhibition of aggregation followed the opposite trend of van der Waals contacts between DNA and amino acids. The difference between NH2-PR and NH2-MR amount in the aggregation inhibition process was mainly controlled by the specific two sets of favorable or derogatory van der Waals contacts between amino acids with adenine or thymine of DNAs. 1. INTRODUCTION DNA-protein interaction is the basic understanding of complex biological systems.1,2 This interaction is quite different from covalent interaction even for the case of specific DNA binding proteins.3,4 The weak interactions, which are responsible for DNA-protein interactions specifically through the amino acids within proteins, are van der Waals contact, hydrogen bonding and water mediated bonding interactions.5 The theoretical predictions6-12 as well as experimental proofs1319 of DNA-protein interactions are quite evident in recent time literature. Scheraga and coworkers carried out the interaction computationally between AApusc among amino acids and DNA with the help of physics based potentials.20 Recently free energy calculation was also performed for amino acids with side chains for the hydroxyapatite growth in the presence of small molecules.21Although amino acids within AApusc have not been compared experimentally all together in any report, their separate detection studies are known in literature.22,23 Chemiluminescence based silver nanoparticle was explored to differentiate the group of selected amino acids, where Thr has been only considered.22 Another differentiation methodology was performed on the basis of interaction with serum albumin, intracellular uptake and cytotoxicity among another group of selected amino acids, where Ser was the only amino acids from the AApusc.23 Gold nanoparticle (AuNP) is well established for its biomolecule recognition activity through the modification of surface plasmon resonance (SPR) property after the growth reac-

tions.24-26 Chiral amino acids play an important role in the development of specific chirality within gold nanoparticle via growth-mediated synthesis.27 This growth-based material development was considered as milestone in the development of device, which can control the light rotation.28 Seed mediated growth of gold nanorods in presence of amino acids showed chiroptical responses in the visible to near infrared region.29 DNA also showed superstructure of nanoparticles for switchable chirality30 and plasmonic nanostructures.31 Among the weak interactions between DNA and amino acids, hydrogen-bonding interaction was well established by experimental methods.32 Recently, we also reported the DNAamino acid hydrogen bonding interaction exclusively by AuNP for detection of single arginine over single lysine in a peptide sequence.33 Although there are few theoretical models5,20,21 for differentiating the AApusc, there is no experimental methodology to differentiate their interactions with DNA till date. In order to differentiate the AApusc by their different extent of van der Waals contact with DNA, time dependent aggregation from AuNP seed was explored after growth of gold nanoparticle in presence of amine modified DNAs (NH2-PR and NH2-MR, Scheme 1A). To the best of our knowledge, this is the first material based experimental approach to differentiate these four amino acids via their van der Waals contacts with DNAs. In this study, the time dependent growth reaction of AuNP was initially performed with AApusc. Out of four AApusc, Ser showed immediate aggregation after the growth, while rest of them show non-aggregated AuNP (Scheme 1B). In presence of higher concentration of amine modified DNA (NH2-PR),34

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the aggregation of the AuNP after the growth was completely inhibited for all AApusc even after the 24 h of the reaction (Scheme 1C). Lowering down the concentration of NH2-PR showed slow aggregation process. In the case of mutated DNA sequence NH2-MR, concentration dependent non-aggregation vs. slow aggregation was observed. All these experimentally data were analyzed and direct correlation with van der Waals contact between amino acids and DNA were observed.

within seconds. The final volume of solution was restricted to 340 µL. Growth reactions of gold nanoparticles with decreasing DNA and L-amino acids. 0.45 nM of gold nanoparticles seed solutions were incubated with different concentrations of DNA for 30 minutes. 9 mM amino acid was added and further incubated for 30 minutes. 3 µL of 200 mM NH2OH (adjusted to pH 5 with NaOH) was added to these solutions and stirred vigorously for 10 minutes. 5 µL of 0.8% (w/v) HAuCl4 was added to these solutions to initiate the reduction reaction. The color change was observed within seconds. The final volume of solution was restricted to 340 µL. Characterization. Absorbance measurements of the solutions were taken using the Synergy micro plate reader (BIOTEK, USA) over range of 400-800 nm. The TEM images of GNPs (gold nanoparticles) were performed using FEI, Technai G2 20 S-TWIN. The sample was drop casted on carbon coated 200 mesh TEM grid. DLS measurements were taken using Zetasizer Nano ZS90 (Malvern instruments) at 1 hour interval over total time of 12 h. DTS application 7.03 software was used to analyze the data.

Scheme 1. A) Chemical structures of amino acids containing polar uncharged side chains (AApusc) and cartoon structures of amine modified DNA (NH2-PR) and its mutant version (NH2MR); B) differentiation of Ser from rest three amino acid via growth reactions of AuNP seed; C) growth reactions of AuNP seed in presence of different concentrations of DNAs and AApusc for time dependent studies of aggregation vs. nonaggregation.

3. RESULTS AND DISCUSSION

2. EXPERIMENTAL SECTION Materials: All the oligonucleotides used in the study were purchased from the GeneX India Bioscience Pvt. Ltd. Hydrogen tetrachloroaurate (III) hydrate (HAuCl4.3H2O) were purchased from the Sigma-Aldrich, Hydroxylamine hydrochloride (NH2OH.HCl) were purchased from SISCO Research Laboratories, Sodium hydroxide was purchased from Thomas Baker and trisodium citrate dihydrate was purchased from Merck chemicals. L-Amino acids were purchased from Himedia Laboratories Pvt. Ltd. The amino acid solutions were preared in 1:1 mixture of ethanol and water. Synthesis of Seed stock solution. The seed solution was prepared as previously mentioned.17 Growth reaction with L-amino acids. 0.45 nM of gold nanoparticles seed solutions were incubated with 9 mM amino acid for 30 minutes. 3 µL of 200 mM NH2OH (adjusted to pH 5 with NaOH) was added to these solutions and stirred vigorously for 10 minutes. 5 µL of 0.8% (w/v) HAuCl4 was added to these solutions to initiate the reduction reaction. The color change was observed within seconds. The final volume of solution was restricted to 340 µL. Growth reactions of gold nanoparticles with DNA and Lamino acids. 0.45 nM of gold nanoparticles seed solutions were incubated with 200 pmol DNA for 30 minutes. 9 mM amino acid was added and further incubated for 30 minutes. 3 µL of 200 mM NH2OH (adjusted to pH 5 with NaOH) was added to these solutions and stirred vigorously for 10 minutes. 5 µL of 0.8% (w/v) HAuCl4 was added to these solutions to initiate the reduction reaction. The color change was observed

The growth reaction was carried out in presence of AuNP seed (16 ± 3 nm), which had been obtained from citrate based reduction of Au(III) salt.34 This seed (0.45 nM) was incubated with AApusc for 30 min at room temperature. The adsorption interaction between AApusc and AuNP depends upon the functional groups present in the amino acids.35 For Ser and Thr, Au-O interaction is responsible, whereas for Asn and Gln, amino group of the side chain is responsible.35 The growth reaction was carried out in presence of hydroxylamine and Au(III) salt

Figure 1. A-B) Absorbance and TEM images of aggregated gold nanoparticle after the growth reaction in presence of Ser; C) Absorbance spectra of non-aggregated gold nanoparticle after the growth reaction in presence of Thr, Asn and Gln; D) TEM image of gold nanoparticle after the growth reaction in presence of Gln.

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The Journal of Physical Chemistry at room temperature. In the case of Ser, the growth reaction resulted in immediate blue solution with dual absorption peaks (Figure 1A). The TEM (Transmission Electron Microscope) image confirmed the formation of aggregated AuNP (Figure 1B). In the case of rest three amino acids, the growth reactions resulted in red color solution due to the formation of non-aggregated AuNP (Figure 1C-D and S1). The selective aggregation in presence of Ser was further confirmed by hydrodynamic radii measurement (Figure S2). All these solutions were kept in dark and distinct changes were observed after 24 h in each case. The aggregated AuNP from Ser mediated growth reaction was precipitated out over time. In the case of other three solutions with Thr, Asn and Gln, colors of the solutions turned blue. We then carefully observed the color changes in these three solutions over time (Figure 2A-C). The development of new peak around 700 nm was very prominent in the case of Thr and Asn. The process was very slow for Gln. This color development in the solution was due to the formation of aggregated AuNP (Figure S3). The careful analysis of absorption at 700 nm (Figure 2D) due to aggregation within first 4 h after the growth reactions for the three amino acids showed the slowest aggregation formation for Gln. However, the absorbance spectra confirmed the involvement of two-stage process during aggregation and a distinct difference was observed after 12 h. The difference in van der Waals volume and accessible surface area within these amino acids36 influenced in the aggregation process, which resulted in the development of color in the solution. Gln, having the highest van der Waals volume of 114 Å3 and accessible surface area 144 Å2 showed the slowest rate of aggregation at the initial stage. Ser with the lowest van der Waals volume 73 Å3 and accessible surface area 80 Å2 exhibited immediate aggregation. On the other hand van der Waals volumes for Thr and Asn are 93 and 96 Å3 respectively and accessible surface area are 102 and 113 Å2 respectively. The aggregation process at the initial stage after the

Figure 2. Time dependent change of absorption spectra due to aggregation of gold nanoparticle after the growth reaction in presence of A) Thr, B) Asn, C) Gln; D) the change of absorbance due to aggregation at 700 nm with time.

Scheme 2. The proposed mechanism of inhibition of aggregation after the growth reaction in presence of 600 nM NH2-PR and 9 mM Ser due to the van der Waals contact between DNA and Ser.

growth reactions in our case could therefore be directly correlated with van der Waals volumes of the amino acids. In contrast, the growth reaction in absence of any amino acid did not show any aggregation within 24 h (Figure S4). This size dependent aggregation process among AApusc could be correlated to the van der Waals force, as this force is directly related to the size of the molecule.37 The above methodology was successful to differentiate Ser from the rest of the three amino acids within AApusc. However, in order to differentiate these amino acids, 600 nM amine modified DNA (NH2-PR) was introduced in the incubation prior to the AApusc incubation. We wanted to introduce the interaction between amino acids and DNA in the growth process. The affinity of the growth was affected in the presence of amine modified DNA. In this case, aggregation of AuNP was inhibited for all the four amino acids (Figure S5 and S6) after the growth reactions in presence of NH2-PR. These remained non-aggregated for even after 24 h (Figure S5). The interaction between DNA and amino acid might be responsible for the less effective concentration of amino acids (Scheme 2) around AuNP for the aggregation process. The introduction of thymine (NH2-MR) in presence of adenine (NH2-PR) of the amine modified DNA sequence was reported to have less effective binding with AuNP.18 We expected that introduction of NH2-MR prior to the amino acid addition would show aggregation with time for all the amino acids due to the fast displacement of less effective NH2-MR from AuNP surface. However, in these cases, the growth reactions in presence of AApusc immediately resulted in non-aggregated AuNP. Interestingly, the solution containing Ser showed slow aggregation with time. This aggregation in presence of Ser was confirmed by the absorbance and TEM image (Figure 3A-C). The change of hydrodynamic radii with time confirmed the slow aggregation in presence of NH2-MR and Ser (Figure 4A). The polydispersity index (PDI) was almost constant with respect to time in the case of Ser mediated growth (Figure S7). The PDI were maximum during the combined treatment of NH2-PR and Ser and minimum during the treatment of Ser alone. In the case of other three amino acids, NH2-MR incubation inhibited the aggregation of AuNP up to 24 h from the growth reactions (Figure S8). The change in hydrodynamic radii for these three amino acids confirmed the



Figure 3. A) Time dependent change of absorption spectra due to aggregation of gold nanoparticle after the growth reaction in presence of NH2-MR and Ser; the TEM images of the same reaction after B) 0 h and C) 10 h. inhibition of aggregation process for both DNA sequences (Figure 4B). The PDI values showed a downtrend with respect to time in the case of Thr and Gln (Figure S9). The combination of NH2-PR or NH2-MR and Thr or Gln showed slightly enhanced or constant values in PDI with respect to time. In the case of Asn, the PDI with respect to time were almost unchanged (Figure S10) and the PDI values were low in absence of any DNA sequence. The surface charge (ζ-potentials) was found to be negative with time in all the cases (Figure S11-14). In absence of any DNA, negative surface charge showed the trend Ser < Thr < Gln < Asn. In the case of NH2-PR, the surface charges were almost constant for all the four amino acids. In the case of NH2-MR, the surface charge was distinctly different in the case of Ser. The overall surface charge data confirmed that the aggregation was successful for the gold nanoparticle with low negative surface charge. In order to rationalize the aggregation difference for

600 nM NH2-MR and NH2-PR with 9 mM Ser, we compared the weak interactions between DNA and Ser. Among the three types of weak interactions, hydrogen bonding and water-mediated bonding affinities do not vary between thymine and adenine with Ser.5 However, the van der Waals contact, which is negligible in the case of adenine-Ser interaction, shows significant interaction in thymine-Ser case.5 This van der Waals contact was responsible for slow aggregation from the combination of NH2-MR and Ser. In order to confirm the presence of van der Waals contact in the time dependent aggregation process with Ser, we lowered down the concentration of NH2-PR to favor the aggregation. On the other hand, we increased the concentration of NH2-MR to inhibit the aggregation in presence of Ser. In the case of NH2-PR, addition of 60 nM DNA solution was required for the aggregation of AuNP after 12 h from the growth reaction, while for NH2-MR, we required 8 µM solution to inhibit the process (Figure S15 and Table1). The effective concentration of Ser, which was required for the aggregation in each case, could be achieved only after fulfilling the requirement of van der Waals contact between Ser and adenine or thymine. Among weak interactions, van der Waals contact3 between DNA and amino acid is known to cover twothird of all interactions for thermodynamic stability. Therefore, 100 times higher concentration of NH2-MR with respect to NH2-PR concentration was justified for the aggregation process in presence of Ser due to more van der Waals contact between Ser and thymine. In order to check the effect of van der Waals effect among the other amino acids of AApusc family, the concentration of NH2-PR and NH2-MR were lowered down from 600 nM to observe the aggregation process. The critical concentrations (Figure S16), which were required for the aggregation process after 12 h, have been summarized in Table 1. The concentration of NH2-PR, which were required for aggregation with amino acids of AApusc family, follows the order Thr < Asn < Gln < Ser. This trend is simply follow the reverse order (Thr > Asn > Gln > Ser) of van der Waals contact between DNA and amino acids of AApusc family.5 The significant difference of NH2-PR concentration in the cases of Gln and Ser could be rationalized with the help of the size of these two amino acids. Table 1. Concentration of minimum amount of amine modified DNAs required for the aggregation after 12 h of growth reactions in presence of 9 mM AApusc. AApusc

Concentration of NH2-PR

Concentration of NH2-MR

60nM 0.4pM 30pM 4nM

7µM 4nM 3pM 30 nM

Ser Thr Asn Gln

Figure 4. Time dependent change of hydrodynamic radii due to aggregation of gold nanoparticle after the growth reaction in presence and absence of NH2-MR and NH2-PR along with A) Ser and B) Thr, Asn and Gln.

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On the other hand, the concentration NH2-MR, which was required for the amino acids of AApusc family, did not follow the similar strategy to that of NH2-PR. In the case of Thr, the concentration of NH2-MR was 104 times more with respect to NH2-PR concentration (Table 1). The


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The Journal of Physical Chemistry concentrations of NH2-MR were 117 and 7.5 times higher respectively with respect to NH2-PR concentration for Ser and Gln. This trend is due to significant difference of van der Waals contact between adenine and thymine with these amino acids. Upon mutation from adenine to thymine, the order of van der Waals contacts show the trend Thr > Ser >Gln, which is similar to our observation. The covalent38 AApusc-AuNP interaction is stronger than the noncovalent5 AApusc-DNA interaction. However, the increasing amount of DNA strand was sufficient to develop weak AApusc-DNA interaction. This weak van der Waals contact inhibited the AuNP surface modification with amino acids, which led to control the aggregation process after the growth reaction. Interestingly, in the case of Asn, the NH2-MR concentration was found to be 10 times less than NH2-PR concentration in the critical amount measurement for aggregation process. This is also similar to the theoretically predicted trend of Asn, where van der Waals contact decreases from adenine to thymine modification.5 CONCLUSIONS In this study we investigated the growth-controlled reactions of gold nanoparticles with amino acids containing polar uncharged amino acids. The growth of gold nanoparticle resulted in aggregation either instantly or slowly with time depending upon the nature of amino acids. The fast or slow aggregation process depends upon the size or van der Waals contact of the amino acids. We systematically studied the effect of the amine modified DNAs in order to control the aggregation of the gold nanoparticles after the growth reactions. The van der Waals contact between amino acids and nucleic bases such as adenine and thymine were explored for the controlled aggregation process of gold nanoparticle at subnanomolar concentration of amine modified DNAs. This demonstration of time dependent aggregation process is the first experimental correlation of theoretically predicted van der Waals contact5 between DNA and amino acids. This current strategy was successfully shown the differentiation of four amino acids containing polar uncharged side chains via time dependent aggregation process in presence of super or subnanomolar concentration of two amine modified DNAs, where adenine in NH2-PR sequence had been replaced with thymine in NH2-MR. ■ ASSOCIATED CONTENT SupportingInformation The Supporting Information is available free of charge on theACS Publications website at DOI: Electronic absorption,TEM images, hydrodynamic radii, PDI andζ-potentials are mentioned in supporting information. ■ AUTHOR INFORMATION Corresponding Author *E-mail: [email protected] ORCID Kalyan K. Sadhu: 0000-0001-5891-951X Notes The authors declare no competing financial interest.

■ ACKNOWLEDGMENTS KKS acknowledges the DST Nanomission (DST/NM/NB/ 2018/237) for funding. ■ REFERENCES (1) Bai, X.; Talukder, P.; Daskalova, S. M.; Roy, B.; Chen, S.; Li, Z.; Dedkova, L. M.; Hecht, S. M. Enhanced Binding Affinity for an i-Motif DNA Substrate Exhibited by a Protein Containing Nucleobase Amino Acids. J. Am. Chem. Soc. 2017, 139, 4611−4614. (2) Gustafsdottir, S. M.; Schlingemann, J.; Rada-Iglesias, A.; Schallmeiner, E.; Kamali-Moghaddam, M.; Wadelius, C; Landegren, U. In Vitro Analyais of DNA-Protein Interactions by Proximity Ligation. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 3067−3072. (3) Smith, A. J.; Thomas, F.; Shoemark, D.; Woolfson, D. N.; Sarvery, N. J. Guiding Biomolecular Inteactions in Cells using de novo Protein-Protein Interfaces. ACS Synth. Biol. 2019, 8, 1284−1293. (4) Wagner, J. R.; Demir, O.; Carpenter, M. A.; Aihara, H.; Harki, D. A.; Harris, R. S.; Amaro, R. E. Determinants of Oligonucleotides Selectivity of APOBEC3B. J. Chem. Inf. Model. 2019, 59, 5, 2264−2273. (5) Luscombe, N. M.; Laskowski, R. A.; Thornton, J. M. Amino Acid-Base Interactions: A Three-Dimensional Analysis of Protein-DNA Interactions at An Atomic Level. Nucleic Acids Res. 2001, 29, 2860−2874. (6) Zanegina, O.; Kirsanov, D.; Baulin, E.; Karyagina, A.; Alexeevski, A.; Spirin, S. An Updated Version of NPIDB Includes New Classifications of DNA-Protein Complexes and Their Families. Nucleic Acid Res. 2016, 44, D144−153. (7) Gapsys, V.; Groot, B. L. de. Alchemical Free Energy Calculations for Nucleotide Mutattions in Protein-DNA Complexes. J. Chem. Theory Comput. 2017, 13, 6275−6289. (8) Chiu, T.-P.; Rao, S.; Mann, R. S.; Honig, B.; Rohs, R. Genome-wide Prediction of Minor-Groove Electrostatic Potential Enables Biophysical Modeling of Protein-DNA Binding. Nucleic Acids Res. 2017, 45, 12565−12576. (9) Stasyuk, O. A.; Jakubec, D.; Vondrasek, J.; Hobza, P. Noncovalent Interactions in Specific Recognition Motifs of Protein-DNA Complexes. J. Chem. Theory Comput. 2017, 13, 877−885. (10) Andrews, C. T.; Campbell, B. A.; Elcock, A. H. Direct Comparison of Amino Acid and Salt Interactions with DoubleStranded and Single-Stranded DNA from Explicit-Solvent Molecular Dynamics Simulations. J. Chem. Theory Comput. 2017, 13, 1794−1811. (11) Gardini, S.; Furini, S.; Santucci, A.; Niccolai, N. A Structural Bioinformatics Investigation on Protein-DNA Complexes Delineates Their Modes of Interaction. Mol. Biosyst. 2017, 13, 1010−1017. (12) Blanco, J. D.; Radusky, L.; Climente-Gonzalez, H.; Serrano, L. FoldX Accurate Structural Protein-DNA Binding Prediction using PADA1 (Protein Assisted DNA Assembly 1) Nucleic Acid Res. 2018, 46, 3852−3863. (13) Li, C.; Tao, Y.; Yang, Y.; Xiang, Y.; Li, G. In Vitro Analysis of DNA-Protein Interactions in Gene Transcription Using DNAzyme-Based Electrochemical Assay. Anal. Chem. 2017, 89, 5003-5007.



(14) Frykholm, K.; Nyberg, L. K.; Westerlund, F. Exploring DNA-Protein Interactions on The Single DNA Molecule Level using Nanofluidic Tools. Integr. Biol. 2017, 9, 650−661. (15) Buxton, K. E.; Kennedy-Darling, J.; Shortreed, M. R.; Zaidan, N. Z.; Olivier, M.; Scalf, M.; Sridharan, R.; Smith, L. M. Elucidating Protein-DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry. J. Proteome Res. 2017, 16, 3433−3442. (16) Millan, C. R.; Acosta-Reyes, F. J.; Lagartera, L.; Ebiloma, G. U.; Lemgruber, L.; Martinez, J. J. N.; Saperas, N.; Dardonville, C.; de Koning, H. P.; Campos, J. L. Functional and Structural Analysis of AT-Specific Minor Groove Binders that Disrupt DNA-Protein Interactions and Cause Disintegration of the Trypanosoma brucei Kinetoplast. Nucleic Acid Res. 2017, 45, 8378−8391. (17) Jeong, K.-B.; Luo, K.; Lim, M.-C.; Jung, J.-Y.; Yu, J.-S.; Kim, K.-B.; Kim, Y.-R. Reduction of DNA Folding by Ionic Liquids and Its Effects on the Analysis of DNA-Protein Interaction Using Solid-State Nanopore. Small 2018, 14, 1801375. (18) Tutkus, M.; Rakickas, T.; Kopustas, A.; Ivanovaite, S.; Venckus, O.; Navikas, V.; Zaremba, M.; Manakova, E.; Valiokas, R. Fixed DNA Molecule Arrays for High-Throughput Single DNA-Protein Interaction Studies. Langmuir 2019, 35, 5921−5930. (19) Öz, R.; Sriram, K. K.; Westerlund, F. A Nanofluidic Device for Real-Time Visualization of DNA-Protein Interactions on The Single DNA Molecule Level. Nanoscale 2019, 11, 2071−2078. (20) Yin, Y.; Sieradzan, A. K.; Liwo, A.; He, Y.; Scheraga, H. A. Physics-Based Potentials for Coarse-Grained Modeling of Protein-DNA Interactions. J. Chem. Theory Comput. 2015, 11, 1792−1808. (21) Xu, Z.; Wei, Q.; Zhao, W.; Cui, Q.; Sahai, N. Essence of Small Molecule-Mediated Control of Hydroxyapatite Growth: Free Energy Calculations of Amino Acid Side Chain Analogues. J. Phys. Chem. C 2018, 122, 4372−4380. (22) He, Y.; Liang, Y.; Yu, H. Simple and Sensitive Discrimination of Amino Acids with Functionalized Silver Nanoparticles. ACS Comb. Sci. 2015, 17, 409−412. (23) Cai, H.; Yao, P. Gold Nanoparticles with Different Amino Acid Surfaces: Serum Albumin Adsorption, Intracellular Uptake and Cytotoxicity. Colloid Surf. B. 2014, 123, 900−906. (24) Ha, T.-L.; Shin, J.; Lim, C. W.; Lee, I. S. Seed-mediated Growth of Gold inside Hollow Silica Nanospheres for Sensing Peroxide and Glucose Concentrations. Chem. Asian. J. 2012, 7, 36−39. (25) Huang, Y.; Zhao, M.; Han, S.; Lai, Z.; Yang, J.; Tan, C.; Ma, Q., Lu, Q., Chen, J., Zhang, X., et al. Growth of Au Nanoparticles on 2D Metalloporphyrininc Metal-Organic Framework Nanosheets Used as Biomimetic Catalysts for Cascade Reactions. Adv. Mater. 2017, 29, 1700102. (26) Zheng, X. T.; Goh, W. L.; Yeow, P.; Lane, D. P.; Ghadessy, F. J.; Tan, Y. N. Ultrasensitive Dynamic Light Scattering Based Nanobiosensor for Rapid Anticancer Drug Screening. Sens. Actuators B. 2019, 279, 79−86. (27) Lee, H.-E.; Ahn, H.-Y.; Mun, J.; Lee, Y. Y.; Kim, M.; Cho, N. H.; Chang, K.; Kim, W. S., Rho, J.; Nam, K. T. Amino-Acid- and Peptide-Directed Synthesis of Chiral Plasmonic Gold Nanoparticles. Nature 2018, 556, 360−365.

Page 6 of 7

(28) González-Rubio, G.; Liz-Marzán, L. M. Peptides Used to make Light-Twisting Nanoparticles. Nature 2018, 556, 313−316. (29) Zheng, G.; Bao, Z.; Pérez-Juste, J.; Du, R.; Liu, W.; Dai, J.; Zhang, W.; Lee, L. Y. S.; Wong, K.-Y. Tuning the Morphology and Chiroptical Properties of Discrete Gold Nanorods with Amino Acids. Angew. Chem. Int. Ed. 2018, 57, 16452−16457. (30) Lan, X.; Liu, T.; Wang, Z.; Govorov, A. O.; Yan, H.; Liu, Y. DNA-Guided Plasmonic Helix with Switchable Chirality. J. Am. Chem. Soc. 2018, 140, 11763−11770. (31) Tan, S. J.; Campolongo, M. J.; Luo, D.; Cheng, W. Building Plasmonic Nanostructures with DNA. Nat. Nanotechnol. 2011, 6, 268−276. (32) Pang, X. F. Properties of Proton Transfer in HydrogenBonded Systems and Its Experimental Evidences and Applications in Biology. Prog. Biophys. Mol. Biol. 2013, 112, 1−32. (33) Lone, S. A.; Sadhu, K. K. Gold Nanoflower for Selective Detection of Single Arginine Effect in a-helix Conformational Change over Lysine in 310-Helix Peptide. Bioconjugate Chem. 2019, 30, 1781−1787. (34) Lone, S. A.; Sadhu, K. K. Formation of Growth-Mediated Gold Nanoflowers: Roles of the Reducing Agent and AmineModified, Single-Strand DNA Sequences. ChemPlusChem 2019, 84, 112−118. (35) Ramezani, F.; Amanlou, M.; Rafii-Tabar, H. Comparison of Amino Acids Interaction with Gold Nanoparticle. Amino Acids 2014, 46, 911−920. (36) Darby, N. J.; Creighton, T. E. Protein Structure; Oxford University Press; Oxford; 1993. (37) Brambilla, N.; Shtabovenko, V.; Castella, J. T.; Vairo, A. Effective Field Theories for van der Waals Interactions. Phys. Rev. D 2017, 95, 116004. (38) Shao, Q.; Hall, C. K. Binding Preferences of Amino Acids for Gold Nanoparticles: A Molecular Simulation Study. Langmuir 2016, 32, 7888−7896.


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Time-Dependent Growth of Gold Nanoparticles: Experimental

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